This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. HIV-1 protease is the target of the most potent anti-viral drugs for the treatment of HIV-1 infection. All of these drugs are the consequence of structure-based drug design. The protease is an ideal target for drug therapy since it processes the Gag and GagPol polyproteins in ten or more unique non-homologous sites that are critical for virion maturation and thus the spread of the virus. Unfortunately, many viable, drug resistant variants of HIV-1 protease have evolved under the selective pressure of drug therapy. Drug resistance at the molecular level is a subtle change in the balance of recognition events between the relative affinity of the enzyme to bind inhibitors and its ability to bind and cleave substrates. In many HIV-1 protease variants multiple site mutations co-evolve to both decrease the affinity of a particular inhibitor and increase the viability and fitness of the enzyme. Crystallographic studies on HIV-1 protease in complex with substrates and inhibitors will prove to be valuable in order to determine molecular interactions that mediate substrate recognition whilst decreasing affinity to a particular inhibitor. Structural insights gained by analyzing high resolution crystal structures of HIV-1 protease in complex with substrates and inhibitors will serve as a guide to develop high affinity inhibitors that are more robust against emerging drug resistant HIV-1 variants.